avinashkarkada / GROMACS-COLAB Public

Notifications You must be signed in to change notification settings
Fork 1
Star 2

Contains gromacs notebooks for MD simulations.

2 stars 1 fork Branches Tags Activity

Name		Name	Last commit message	Last commit date
Latest commit History 25 Commits
APO_MD_GROMACS.ipynb		APO_MD_GROMACS.ipynb
PDB_FIXER.ipynb		PDB_FIXER.ipynb
PL_CHARMgui_GROMACS.ipynb		PL_CHARMgui_GROMACS.ipynb
PL_MD_GROMACS.ipynb		PL_MD_GROMACS.ipynb
README.md		README.md
g_mmpbsa.ipynb		g_mmpbsa.ipynb
gromacs.tar.gz		gromacs.tar.gz

Repository files navigation

GROMACS-COLAB

Contains gromacs notebooks for MD simulations.

APO, pure protein system simulation: https://colab.research.google.com/drive/1jidHa0C0NqLzkTZrYLveM8Y3zvXUzX0C?usp=sharing
Protein-ligand Charmm gui gromacs output simulation: https://colab.research.google.com/drive/1OaqTJhZBQTLixUZqYF24QiyED4beEhA-?usp=sharing
Protein-ligand gromacs simulation: https://colab.research.google.com/drive/1jc9SvLstJjBTk5ZsEz9f7D_VjWjJYmuS?usp=sharing
PDB fixer to add missing residues and fix your pdb: https://colab.research.google.com/github/avinashkarkada/GROMACS-COLAB/blob/main/PDB_FIXER.ipynb
MMPBSA calculations using g_mmpbsa: https://colab.research.google.com/github/avinashkarkada/GROMACS-COLAB/blob/main/g_mmpbsa.ipynb